I am trying to use the Kallisto aligner to run differential exon usage on my dataset. I want to run DEXSeq but am running into an error. Kallisto's GenomeBam does not include an NH tag so DEXSeq's dexseq_counts.py command refuses to run. When trying with Kallisto's PseudoBam the script reports them all as empty, likely due to the coordinates not matching up as PseudoBam doesn't project to genomic coordinates. I was wondering if there is some work around or changing dexseq_counts.py to not require the NH tag?